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<DIV><FONT face="MS UI Gothic" size=2>Thank you Tsjerk;</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>I followed your advice, and it looks
working well.</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>Cheers,</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>Hiromichi</FONT></DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt MS UI Gothic">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt MS UI Gothic; font-color: black"><B>From:</B>
<A title=tsjerkw@gmail.com href="mailto:tsjerkw@gmail.com">Tsjerk
Wassenaar</A> </DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>Sent:</B> Wednesday, June 14, 2006
8:13 PM</DIV>
<DIV style="FONT: 10pt MS UI Gothic"><B>Subject:</B> Re: [gmx-users] Error:
Not enough ref_t and tau_t values</DIV>
<DIV><BR></DIV>Hi Hiromichi,<BR><BR>It is likely that you have some groups
which are not covered by "Protein" and "Other". You can use "Protein" and
"Non-Protein" in stead. But make sure that the two groups correspond to two
distinct groups in your system. You may run into trouble if you have some
non-standard residue in your protein which will end up in the "Non-Protein"
group. <BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>
<DIV><SPAN class=gmail_quote>On 6/14/06, <B class=gmail_sendername>Hiromichi
Tsurui</B> <<A
href="mailto:tsurui@med.juntendo.ac.jp">tsurui@med.juntendo.ac.jp</A>>
wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<DIV>
<DIV bgcolor="#ffffff">
<DIV><FONT face="MS UI Gothic" size=2></FONT>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3>Dear all;</FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3></FONT></FONT></SPAN> </P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3>I am trying to calculate the binding free energy of an
MHC-molecule and a peptide by thermodynamic integration method. The system
contains binding domain of MHC molecule, a peptide presented on it,
water-molecules (about 13,000), and ions (Na+ and Cl- at
PBS-concentration).</FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3>After energy minimization, I tried to equilibrate the
system with the mdp-file as follows, and an error-message appeared as
such;</FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3>"Fatal error.</FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt; TEXT-INDENT: 10.5pt"><SPAN lang=EN-US><FONT
face="MS UI Gothic" size=2><FONT size=3>Not enough ref_t and tau_t
values."</FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt; TEXT-INDENT: 10.5pt"><SPAN lang=EN-US><FONT
face="MS UI Gothic" size=2><FONT size=3>How should I change the conditions
?</FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3></FONT></FONT></SPAN><FONT face="MS UI Gothic"
size=2></FONT> </P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3><FONT face="MS UI Gothic">Many thanks for your
help.</FONT> <FONT face="MS UI Gothic">
</FONT></FONT></FONT></SPAN></P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT face="MS UI Gothic"></FONT></FONT></SPAN><FONT
face="MS UI Gothic" size=2></FONT> </P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT size=3></FONT></FONT></SPAN> </P>
<P style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US><FONT face="MS UI Gothic"
size=2><FONT
size=3>cpp<SPAN>
</SPAN>=<SPAN>
</SPAN>/lib/cpp<BR>define<SPAN>
</SPAN>=<SPAN>
</SPAN><BR>integrator<SPAN>
</SPAN>=<SPAN>
</SPAN>md<BR>tinit<SPAN>
</SPAN>=<SPAN>
</SPAN>0.0<BR>dt<SPAN>
</SPAN>=<SPAN> </SPAN>0.002<SPAN>
</SPAN><BR>nsteps<SPAN>
</SPAN>=<SPAN> </SPAN>100000<SPAN>
</SPAN><BR>nstcomm<SPAN>
</SPAN>=<SPAN>
</SPAN>1<BR>nstxout<SPAN>
</SPAN>=<SPAN>
</SPAN>50000<BR>nstvout<SPAN>
</SPAN>=<SPAN>
</SPAN>50000<BR>nstfout<SPAN>
</SPAN>=<SPAN>
</SPAN>0<BR>nstlog<SPAN>
</SPAN>=<SPAN>
</SPAN>10000<BR>nstenergy<SPAN>
</SPAN>=<SPAN>
</SPAN>250<BR>nstxtcout<SPAN>
</SPAN>=<SPAN>
</SPAN>10000<BR>xtc_precision<SPAN>
</SPAN>=<SPAN>
</SPAN>1000<BR>xtc_grps<SPAN>
</SPAN>=<SPAN>
</SPAN>Protein<BR>energygrps<SPAN>
</SPAN>=<SPAN> </SPAN>Protein
other<BR>nstlist<SPAN>
</SPAN>=<SPAN>
</SPAN>5<BR>ns_type<SPAN>
</SPAN>=<SPAN>
</SPAN>grid<BR>pbc<SPAN>
</SPAN>=<SPAN>
</SPAN>xyz<BR>rlist<SPAN>
</SPAN>=<SPAN>
</SPAN>0.9<BR>coulombtype<SPAN>
</SPAN>=<SPAN>
</SPAN>Reaction-Field<BR>epsilon_r<SPAN>
</SPAN>=<SPAN>
</SPAN>78.0<BR>rcoulomb<SPAN>
</SPAN>=<SPAN>
</SPAN>1.4<BR>vdw-type<SPAN>
</SPAN>=<SPAN>
</SPAN>Cut-off<BR>rvdw<SPAN>
</SPAN>=<SPAN>
</SPAN>1.4<BR>tcoupl<SPAN>
</SPAN>=<SPAN> </SPAN>Berendsen<BR>tc-grps<SPAN>
</SPAN><SPAN> </SPAN>=<SPAN>
</SPAN>Protein
other<BR>ref_t<SPAN>
</SPAN>=<SPAN> </SPAN>300
300<BR>tau_t<SPAN>
</SPAN>=<SPAN> </SPAN>0.1
0.1<BR>pcoupl<SPAN>
</SPAN>=<SPAN>
</SPAN>Berendsen<BR>tau_p<SPAN>
</SPAN>=<SPAN>
</SPAN>1.0<BR>compressibility<SPAN>
</SPAN>=<SPAN>
</SPAN>4.6e-5<BR>ref_p<SPAN>
</SPAN>=<SPAN>
</SPAN>1.0<BR>gen-vel<SPAN>
</SPAN>=<SPAN>
</SPAN>yes<BR>gen-temp<SPAN>
</SPAN>=<SPAN>
</SPAN>300<BR>gen-seed<SPAN>
</SPAN>=<SPAN>
</SPAN>$RANDOM<BR>constraints<SPAN>
</SPAN>=<SPAN>
</SPAN>all-bonds<BR> </FONT></FONT></SPAN></P></DIV>
<DIV><FONT face="MS UI Gothic" size=2>Hiromichi Tsurui MD, PhD<BR>Dept.
Pathology, <BR>Juntendo
University<BR>Phone:81-3-5802-1039<BR>Fax:81-3-3813-3164<BR><A
onclick="return top.js.OpenExtLink(window,event,this)"
href="mailto:tsurui@med.juntendo.ac.jp"
target=_blank>tsurui@med.juntendo.ac.jp</A></FONT></DIV></DIV></DIV><BR>_______________________________________________<BR>gmx-users
mailing list <A
onclick="return top.js.OpenExtLink(window,event,this)"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A
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href="http://www.gromacs.org/mailman/listinfo/gmx-users"
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</A><BR><BR></BLOCKQUOTE></DIV><BR><BR clear=all><BR>-- <BR><BR>Tsjerk A.
Wassenaar, M.Sc.<BR>Groningen Biomolecular Sciences and Biotechnology
Institute (GBB)<BR>Dept. of Biophysical Chemistry<BR>University of Groningen
<BR>Nijenborgh 4<BR>9747AG Groningen, The Netherlands<BR>+31 50 363 4336<BR>
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